SMTL ID : 9g6w.1

L-SIGN CRD in complex with Man96.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2~{R},3~{S},4~{R},5~{S},6~{S})-6-(2-chloroethyloxy)-2-(hydroxymethyl)-5-[4-[(imidazolidin-2-ylideneamino)methyl]-1,2,3-triazol-1-yl]oxane-3,4-diol

01.1: 11 residues within 4Å: Chain A: F.63, E.97, N.99, S.101, E.104, E.108, N.115, D.116, N.117, N.123 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.104, A:E.108, A:N.115, A:N.115, A:N.117 01.7: 12 residues within 4Å: Chain B: F.63, E.97, N.99, S.101, E.104, E.108, N.115, D.116, N.117, V.121, N.123 Ligands: CA.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.99, B:S.101, B:E.104, B:E.108, B:N.115, B:N.115, B:N.117, B:N.123

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.97, N.99, E.104, N.115, D.116 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.97, A:E.104, A:D.116, A:D.116 CA.3: 6 residues within 4Å: Chain A: D.70, E.74, N.100, E.104, D.105 Ligands: CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.70, A:D.70, A:E.104, A:D.105, H2O.1 CA.4: 5 residues within 4Å: Chain A: E.74, N.100, N.103, D.105 Ligands: CA.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.74, A:D.105, A:D.105, H2O.1, H2O.1 CA.8: 6 residues within 4Å: Chain B: E.97, N.99, E.104, N.115, D.116 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.97, B:E.104, B:D.116, B:D.116 CA.9: 6 residues within 4Å: Chain B: D.70, E.74, N.100, E.104, D.105 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.70, B:E.74, B:E.104, B:D.105, H2O.5 CA.10: 4 residues within 4Å: Chain B: E.74, N.103, D.105 Ligands: CA.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.74, B:D.105, B:D.105, H2O.4

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: F.19, S.21, N.22, S.23, W.125 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.62, F.63 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 2 residues within 4Å: Chain B: D.120, D.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.120, B:D.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazzoli, G. et al., L-SIGN CRD in complex with Man96. To be published

Release Date

2025-07-30

Peptides

Isoform 1 of C-type lectin domain family 4 member M: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 1 of C-type lectin domain family 4 member M

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